羅莎琳德共識和檔案

Question

我想從這裏http://rosalind.info/problems/cons/

我的劇本充滿計數器列表和輸出相同長度的字符串共識解決這個問題。我不認爲有數學或指標錯誤發生，並且遇到了困難。我的代碼：

with open('C:/users/steph/downloads/rosalind_cons (3).txt') as f: 
    seqs = f.read().splitlines() 

#remove all objects that are not sequences of interest 
for s in seqs: 
    if s[0] == '>': 
     seqs.remove(s) 

n = range(len(seqs[0])+1) 

#lists to store counts for each nucleotide 
A, C, G, T = [0 for i in n], [0 for i in n], [0 for i in n], [0 for i in n] 

#see what nucleotide is at each index and augment the 
#same index of the respective list 
def counter(Q): 
    for q in Q: 
     for k in range(len(q)): 
      if q[k] == 'A': 
       A[k] += 1 
      elif q[k] == 'C': 
       C[k] += 1 
      elif q[k] == 'G': 
       G[k] += 1 
      elif q[k] == 'T': 
       T[k] += 1 
counter(seqs) 

#find the max of all the counter lists at every index 
#and add the respective nucleotide to the consensus sequence 
def consensus(a,t,c,g): 
     consensus = '' 
     for k in range(len(a)): 
      if (a[k] > t[k]) and (a[k]>c[k]) and (a[k]>g[k]): 
       consensus = consensus+"A" 
      elif (t[k] > a[k]) and (t[k]>c[k]) and (t[k]>g[k]): 
       consensus = consensus+ 'T' 
      elif (c[k] > t[k]) and (c[k]>a[k]) and (c[k]>g[k]): 
       consensus = consensus+ 'C' 
      elif (g[k] > t[k]) and (g[k]>c[k]) and (g[k]>a[k]): 
       consensus = consensus+ 'G' 
      #ensure a nucleotide is added to consensus sequence 
      #when more than one index has the max value 
      else: 
       if max(a[k],c[k],t[k],g[k]) in a: 
        consensus = consensus + 'A' 
       elif max(a[k],c[k],t[k],g[k]) in c: 
        consensus = consensus + 'C' 
       elif max(a[k],c[k],t[k],g[k]) in t: 
        consensus = consensus + 'T' 
       elif max(a[k],c[k],t[k],g[k]) in g: 
        consensus = consensus + 'G' 
     print(consensus) 
     #debugging, ignore this --> print('len(consensus)',len(consensus)) 
consensus(A,T,C,G) 

#debugging, ignore this --> print('len(A)',len(A)) 

print('A: ',*A, sep=' ') 
print('C: ',*C, sep=' ') 
print('G: ',*G, sep=' ') 
print('T: ',*T, sep=' ') 

謝謝您的時間

Answer 1

• 有以下行錯誤：

  N =範圍（LEN（seqs [0]）+ 1）

這導致序列太長（填充額外A和4倍0）。刪除+1，它應該工作。

• 此外，您的輸出中有兩個空格，請在您的打印語句中刪除:之後的空格。
• 如果你修復了這兩行，它將適用於這個例子，但是對於比一行更長的序列將會失敗（就像真正的例子）。

嘗試合併線條與類似下面的剪斷：

new_seqs = list() 
for s in seqs: 
    if s.startswith('>'): 
     new_seqs.append('') 
    else: 
     new_seqs[-1]+=s 
seqs = new_seqs 

，並再次嘗試。